There is another way. (Probably easier to). Apache and the browser won't time out as long as data is being sent. So send some data...

#!/usr/bin/perl

$| = 1;

# thousands of ways to do this
print "Content-type: text/html\n\n";

### set up an alarm
my $timeout = 4*60; # apache normally times out after 5 min
print "<!--\n";  # hide output
$SIG{ALRM} = sub{ print ".\n"; alarm($timeout); };
# the timeout will send something to the browser every
# now and then to keep it from timing out

alarm($timeout);
&do_something_heinous();
alarm(0);
print "-->\n";  # don't need to hide output anymore

print "All done\n";
exit;

sub do_something_heinous {
  sleep(6 * 60);
}
[download]

My company actually has a module that we can use to wrap around this. It works great. (Actually, I typed this code in from memory -- our servers are down from a storm -- hope it compiles, but the idea should be intact).

my @a=qw(random brilliant braindead); print $a[rand(@a)];